Project S Walker
by Haley Elizabeth James
Summary: 21 year ago, Sarah Walker left the CIA and Chuck to protect her daughter, Spencer. Now Spencer has been recruited into the organization her mother left behind. Unknowingly, Chuck has chosen his daughter to be apart of his team and to train her. How will Sarah react when she realizes? Will Chuck figure out the connection? What is Spencer's purpose on the team?
1. Chapter 1: Spencer Versus the Interview

_I do not own any characters from chuck_

Project S. Walker

 **Chapter 1: Spencer versus the Interview**

Spencer spun around after tying up her Chuck Taylor black high tops while looking into the mirror to pull her long blonde hair up into a pony tail. Today was her twenty first birthday, and she was about to have the most important interview of her life.

Let's take it back to twenty one years ago, Sarah Walker had walked away from everything she had ever known, for her daughter. She left the CIA, and Chuck, the unknowing father of this precious child. Today was the day that Sarah had started her life over, to protect Spencer to make sure that there was a normal life for her daughter, unlike the life she had. Sarah had begun using the Walker last name for Spencer as a way to still feel connected to her old life. She had told Spencer that the last name Walker was connected to a very important person in her life. Spencer believed the last name was connected to her father. Sarah was currently using the last name Stiles. They lived in a small bungalow just past Laguna Beach, which is ironic considering she has left the spy life behind her. She had died her hair a deep brunette colour and had opted for darker makeup to limit her appearance that someone may recognize. Before Spencer was born, Sarah had managed to create this persona so that Spencer may never be tracked down as her child.

"Mornin' Mom" Spencer entered the kitchen with a huge grin on her face.

"Happy Birthday Spence!" Sarah said, pulling a plate of waffles and bacon out

"Thanks Mom, you really didn't have to do this" Spencer said

"I know, but your 21, you only turn 21 once!" Sarah grinned

"And hopefully I will get the job today to make everything so much better" Spencer replied

"A job interview? You have to tell me everything" Sarah questioned

"I will tonight, I should get going" Spencer said before leaving the house.

Spencer got into her Volkswagen Jetta and began her commute to her job interview. She hadn't really wanted to tell her mom about the location of said interview as it could cause a major change in their relationship. The job interview was located in Burbank, which would mean that she'd probably have to move out because the commute from Laguna would be interesting with all the traffic.

Meanwhile at a not so far Buymore located in Burbank, Chuck Bartowski and John Casey were preparing for the treacherous day of three interviews for the candidates that would be trained to join on their team. They had chosen to interview individuals that were different from the normal CIA and NSA recruits. Chuck had requested to allow John and himself to train the new team member so that trust could be the basis of the team. John hadn't originally agreed to this but after countless harassing attempts by Chuck and Morgan he said yes.

"Bartowski, you'd think after 21 years. They would have gotten rid of you" Casey stated with a straight face.

"Hey, I'm smarter than I look" Chuck replied. Chuck had been through a lot in the past two decades, lost the love of his life and the teammate he could never replace. He often did think about Sarah, and wished things would have worked out differently. To his knowledge Sarah had died during a solo mission in Paris. While Chuck was lost in his thoughts and petite blonde hair, blue eyes woman entered the Buymore. As Chuck began to day dream, he felt a jabbing feeling in his ribs.

"Show time" Casey smiled

Chuck walked over to the interviewer and introduced himself. "Hello, My name is Chuck are you here for an interview?"

"Hey I'm Spencer, I guess I'm here for the interview. I didn't expect it to be in the Buymore" Spencer spoke.

"No one ever does, if you would follow me this way we can begin the process" John said pointing to the main office in the Buymore.

The three gathered in the office and sat down. "Now this isn't going to be like any normal interview you have had before" Chuck spoke as he stared intently at the woman.

"I figured as we are in a Buymore" Spencer sarcastically added

"After completely those competency quizzes, you have been selected as one of the top 3 candidates to join our team" John explained.

"And when we ran your name through our database there were no hits, so you have been cleared to entered castle so that we can begin the actual interview in castle" Chuck responded

Spencer, who was beyond confused, just went along with it. They walked into the locker room. Casey went to his locker, looks around and punched in a combo.

"Welcome to Castle" Chuck said

They sat Spencer in front of a large screen. The screen turned on and a picture of an angry redhead appeared.

"Hello, Spencer. I am Director Beckman with the NSA in conjunction with the CIA"

"Wait this is for the CIA?" Spencer sat there puzzling

"According to the quizzes you completed before this meeting has shown you to be an excellent candidate for this team"

"Woah" Spencer placed her hands on her face and took a breath

"I know this is a lot, and you still have a lot of training to complete with the other candidates in order to develop your abilities" Beckman continued

"Yes Ma'am" Spencer responded.

"Well I leave you to your team Bartowski and Casey keep me updated" Beckman stated before the scene went blank. Spencer sat in the chair taking in all the information she had just been given, it was a lot to process. She was going to a CIA agent and was perplexed about the situation.

"Beckman is a lot to handle, there were many reasons why you were picked to be a potential asset to this team" Chuck said with a smile.

"While you're in training you will be given a cover job and an apartment here in Burbank, this cover is your job that you tell your family you have" Casey spoke assertively.

"I understand" Spencer replied

"Training begins in two days, and here is the key and address to your apartment" Casey said before handing the key to Spencer

"After reviewing your past education, your cover will be as a personal trainer at a Gym next door" Chuck stated, showing Spencer a pamphlet to read so she could be familiar with the job for when her family questions this job. Spencer nodded and left shortly after.

"Spencer Walker seems familiar doesn't she?" Chuck asked.

"Bartowski, they all seem familiar after too many years" Casey snarled.

Chuck was not convinced and decided to review Spencer's file before making a decision about this feeling he felt. After careful deliberation, Chuck realized there wasn't any data to connect Spencer to his past love. He closed the file and smiled, it will be nice to have some new talent joining the team. He had high hopes for Spencer as her scores were the highest recorded in the CIA quizzes.

 _A/N: Let me know what you think, review if you have any ideas for the other two candidates or story line ideas!_


	2. Chapter 2: Spencer Versus the First Day

**Chapter 2: Spencer Versus the First Day**

Spencer gently tapped her index finger on the hardwood of the kitchen table. She was having difficulty deciding on how to break this news to her mother. She knew that her mom would be concerned about the sudden job and moving.

Sarah appeared at the base of the stairs, she was intently watching Spencer deep in thought. Sarah slipped a black hair tie off her wrist before bringing it up to her long brown hair, she glanced in the mirror. Her face wasn't as bright as it once before raising a child had turned out to be a lot more difficult than being an international spy.

"Hey Spence, do you want to go for a run?" Sarah asked. Spencer pondered this question; a run would be the best situation to tell her mother about the job.

"Sure, why not" Spencer replied. Once they both changed they began their run to the beach to enjoy the coastal view. Spencer thought during the run about how exactly to explain the situation. She glanced over at her mom, noticed she was lost in thought as well.

Sarah couldn't help but notice something was different, and it was definitely bothering her. Once they made it to the rest stop.

"How'd that interview go today?" Sarah asked

"It was great, I got the job" Spencer smiled

"That is wonderful, what is the job?" Sarah questioned

"I am going to be a personal trainer in Burbank" Spencer stated proudly

"Burbank is a little far don't you think?" Sarah asked concernedly as she had another important reason why Burbank would be a bad idea. Chuck lived there and if they were to ever meet it would ruin everything she had worked for to protect Spencer.

"Well about that, I've been provided with an apartment as part of my contract" Spencer spoke slowly, trying not to overwhelm her Mom.

"Wow, seems like you've found a great job" Sarah said realizing that she would eventually have to allow her little girl to leave the nest. Burbank is a big place there was no way she'd run into Chuck, if Chuck was still in Burbank. Sarah had given up long ago on keeping tabs on Chuck, she had felt bad about the entire situation but she knew it was for the best. The spy life was no life for a child, it was better this way.

"Thanks for being so supportive, I think this will be a step forward in life" Spencer smiled.

"I'm proud, and you're only an hour away. That means we can still hang out" Sarah replied.

A few days later, Spencer lifted the final box of her things out of the back of her Jetta and closed the trunk softly. She couldn't believe that she was going to be part of the CIA. Her mother had taken the news oddly well. They apartment they had provided was fully furnished and had an awesome location close to the beach, which was an added bonus. The training was beginning in a few hours, so she decided to go for a morning jog before heading off to the first day of the rest of her life.

 _Beep Beep._ Her phone buzzed on the table, she looked down and saw a message from her Mom.

" _Hey Sweetie, hope your settling in okay, and good luck on your first day"_ Spencer smiled before heading out on her run. Once Spencer had left, Sarah appeared from behind car. She was dressed in jeans and a leather jacket with a baseball cap, that she pull down so her face would not been seen. She has carefully made her way to the front door of Spencer's apartment and picked the lock. Sarah couldn't help but smile when she had unlocked the lock, she still had it. She surveyed the apartment and noticed a file sitting on the table she curiously reviewed the information; it was about the gym that Spencer was now working at. She continued to snoop through the apartment and nothing jumped out at her. Sarah heard the turn of a key on the door knob and she hid in a closet so that Spencer would not overreact about the situation. Sarah decided she must follow Spencer to ensure her safety just for today at least.

Sarah silently watched for the crack of the door as her daughter grabbed her gym back and headed out of the apartment. She had a feeling that this was a little strange to be following her child but it was for her safety. Sarah had a sigh of relief when she saw Spencer walk into the gym. At least for the next few hours Spencer was working as a personal trainer and not potentially going to run into Chuck.

Spencer's instructions to enter castle were quite simple, walk in through the gym and head to the back room and enter through the set of lockers. She took a deep breath before entering castle, at the table she sat talking to the Director sat about five new faces, Chuck and Casey.

"Nice of you to join us Spencer" Casey said pointing to an empty seat.

"Woah, Castle extends from the Buymore to the gym?" Spencer asked

"Lots of government agencies have headquarters located underground" Casey stated

"Welcome Candidates to our team, Our NSA and CIA team members are also present today and will be serving as your handlers until you are fully trained" Chuck spoke

"Now you're probably wondering why this is not your normal training exercise" Casey pointed to the large glass board behind him. That had a variety of skills outlined.

"The agencies have allowed us to create a very specific team, for in which one of you candidates will become the fourth and final member of the team. This team needs a certain type of asset, that is the reasoning behind allowing you to be trained by us" Chuck stated

"Unfortunately I cannot release the specifics of this asset as it is currently above your clearance level" Casey firmly said prior to reaching for a file on the table. "Agent Sean Hastings you will be assisting Spencer Walker with her training and be posing as her boyfriend for protective reasons" Casey stated. Spencer turned her head and made eye contact with a very attractive man with green eyes and blonde hair. He had a slew of freckles on his nose. The agent smiled and nodded.

"Jeffery Woo you have been paired with Agent Aaron Michaels and you to will be covering as roommates" Chuck smiled

"And Connor State you will be partnered with Agent Emily Clarke and will be covering as a couple" Casey finally stated lastly.

"Okay why don't you guys take the afternoon and get to know your handlers, meet back here tomorrow morning" Chuck smiled before everyone stood up and begin to pack up there things and head for the door.

Chuck sat there believing that one of these candidates would be the next intersect. He knew the ability needed to make a great intersect, and the type of personality needed. The next few weeks would test individual ability to best decide the next intersect. Chuck raised his hand to head and rested for a moment. After losing Sarah in the mission, he had thrown himself into work to figure the killer that had stolen his beautiful wife from him. This new intersect would finally be able to help him.

Spencer and her handler Sean had made a plan to meet up later this evening to get to know each other. Spencer had suggested her apartment as a low key option and Sean had agreed. When Spencer had left the gym, Sean had offered to walk her to her car; Spencer had given him a puzzling look.

"It's for the cover, Walker don't worry" Sean softly whispered

"Sorry, this is all a lot" Spencer said softly

"Just follow my lead, I promise everything will be okay" Sean said as he opened the door and pointed for Spencer to go.

"Thank you, such a gentleman." Spencer grinned.

"Not a problem, it's always a pleasure to hold the door from such a beautiful woman" Sean smiled. They made eye contact and Sean's smiled turned into a smirk. They continued to walk towards the car and once they arrived at the Jetta. "I was thinking maybe I could call you sometime? Maybe we can go for coffee sometime?"

"Yeah I would love to" Spencer smiled and gave Sean her number. Shortly after Sean went to hug Spencer, which of course Spencer accepted because even his muscles had muscles and she was a sucker for freckles. As he wrapped his arms around her she couldn't help but feel safe in those strong arms.

"Nice job, I will see you tonight" Sean whispered before letting go and walking away.

Spencer stood in place for a second before getting into her car. A cover life would be a lot more work than she thought, but it didn't help that Sean was very cute and very much her type which could be dangerous especially in this line of employment.

Sarah who was sitting in her car the parking lot had watched the entire interaction between Spencer and this man. She couldn't help but feel a sense of relief seeing Spencer meet someone. Her daughter tended to keep her relationships private from her and it was nice to see such a happy smile on her face. Sarah was starting to wonder if she was overreacting. She decided she would keep an eye on Spencer for a few more hours before she would stop spying on her.

 _A/N: Hey Everyone! Thank you for the reviews! I appreciate the feedback. In this chapter I decided you would find out about the reason of the untraditional training, is because it's for a new intersect! I have taken the rest of the ideas and will be making some more interesting chapters coming up. I hope you enjoyed this chapter!_


	3. Chapter 3: Spencer Versus the First Date

**Chapter 3: Spencer versus the First Date**

Spencer stood on a chair attempting to hang a few picture frames before her "date" with her handler Sean. She had put on a pair of jeans that had a ripped knee and navy tank top that fit her body perfectly. Her hair slightly curled that hung nicely over her shoulders. As she was reaching to hang the last photo, there was a knock on the door. "Come on in" Spencer yelled as she began to step down from the chair.

Sean opened the door and greeted Spencer with flowers in hand. He wore a light blue polo and a pair of khakis. "Thanks, you didn't need to" Spencer smiled before taking the flowers over to her kitchen to put them into a vase.

"I know that getting used to having a handler is difficult so I treat the first date, just like any other date." Sean replied before he glanced around the apartment

"Well a first date is all about getting to know each other so it makes sense" Spencer replied before pouring a bag of chips into a bowl and twisting open a jar of salsa.

"A girl that has snacks ready is always great to have around" Sean smiled before taking a seat on the couch.

"What now?" Spencer asked

"We just hang out, unfortunately as spies were not supposed to share information from the past" Sean replied. The two sat and discussed liked and dislikes for what felt for minutes was actually more like hours. Until there was an unexpected knock at the door. Spencer stood up and went over to the door as she peaked through the peep hole, she noticed it was her mom. She turned to Sean mouthing to him that it was her Mom.

Spencer began to open the door "Hey Mom, what are you doing here?" Spencer asked

"Well it has been a few days so I'd figured I'd bring dinner?" Sarah said as she held up two plastic bags of Chinese food. "I brought chicken Lo Mein!" Sarah smiled before she pushed past Spencer to enter the apartment. "This apartment is wonderful, do you have any wine?" Sarah said before placing the food on the table.

"Well I guess I should get going" Sean said standing up off the couch as he began to walking towards Spencer to say good bye.

"Why leave there's lots of food! I'm Sarah Stiles, Spencey's Mom" Sarah said walking over to Sean and extending her arm, Sean shook her hand with a smile.

"Nice to meet you Ms. Stiles, I'm Sean. Only if it's okay with Spencer" Sean turned his attention towards Spencer.

"Well your already here, might as well stay" Spencer said as she pulled Sarah into the kitchen. Sarah followed with a smile.

"Mom, I like this guy please don't mess it up" Spencer whispered, although nothing could mess this up because it was a cover. Spencer believed she should at least sell the cover to her most important person.

"Don't worry so much Spen, also he is really cute good job!" Sarah stated before taking the plates out to the table. Spencer followed behind with a bottle of red wine and three glasses. The three sat down at the round wooden table and served up the meal. "So Sean how'd you meet Spencer?" Sarah asked with a grin although she thought she already knew the answer because of earlier today.

"I'm actually a member of the gym, and met her today. I thought she was really cute and sweet I asked if she wanted to hangout" Sean explained reaching his hand over to Spencer's and laying it on it. Spencer smiled Sean was trying to sell this just as much as she was.

"And I just think boys with freckles are so cute" Spencer stated

"Well isn't that adorable" Sarah smiled before taking around bite of dinner. She noticed how intently Spencer was watching as her began to pour another glass of wine for herself. Her baby girl was smitten with this boy. But her motherly instinct was also setting in; there was no way she was leaving this apartment tonight as she didn't want her daughter to rush things.

 _Buzz Buzz_. Sean's phone began to ring; he stood up from the table and answered it before exiting into the courtyard of the apartment.

"It's probably the bank" Spencer told her mother before taking her empty plate to the kitchen and slipping out the window into the courtyard. "Hey what was that about?" Spencer said walking up beside Sean.

"You need to go back inside and tell your Mom that we're going for a walk and you'll be back in a little while" Sean stated

"Why?" Spencer questions

"Chuck is coming, something about reviewing your file together" Sean said pushing Spencer towards the window. She climbed back through the window and walked out of the kitchen to the table.

"Sean and I are going for a walk, I'll be back in like an hour" Spencer said grabbing her coat and heading for the door. Once the door shut behind Spencer, Sarah thought about following them one last time and decided against it as she needed to put some faith into her daughter.

Sean and Spencer walked about a block before turning down a darkly lit street that had only one house at the end. The front light flickered as they approached the front steps. Spencer wondered why Chuck had called them, so late but she figured it is all part of the job. Sean reached into his pocket and pulled out a ring of keys swing through the multiples of keys to find the correct one. He slipped the key into the lock and turned the door knob. He turned behind him and grabbed Spencer's hand tugging for her to follow.

"I'm getting a bit of horror movie vibes from this light" Spencer whispered

"No need to whisper this is my house" Sean said as he flicked the light on. "I've been meaning to fix that light" Sean smiled. Moments later a car pulled into the driveway and Chuck appeared at the door.

"Sean, Spencer I hope you have enjoyed getting to know each other" Chuck said as he entered the house, carry a briefcase.

"Yeah we were just having dinner and hanging out with the surprise mom visit" Sean spoke in a joking manner

"My mom isn't used to me not being at home, I expected she'd show up" Spencer added

"Is your cover still intact?" Chuck asked

"Yeah my mom doesn't think anything of it" Spencer responded

"Okay, well the reason I am here is because as a candidate you have a chance to review your own file and a file of one of our former agents" Chuck said as he opened his briefcase.

"This is what the emergency was about?" Sean responded.

"There is a protocol I like to follow when training the potential assets" Chuck answered before returning his attention to Spencer. "The purpose of this exercise is to determine the other agent's weak points, as well as becoming in tune with your own weakness to further growth."

"Alright, so I take these files and read them" Spencer said as Chuck handed them to her.

"Not only do you read them, I want you to live, breath and sleep as if your life depended on protecting these files." Chuck stated very clearly.

"As an agent you will be required to provide protection to a magnitude of things, this is seeing if you have the strength and caring attitude that will make you an excellent asset to the team" Sean interrupted

"Thank you Sean. Spencer at any unsuspecting time someone may attempt to take these from you. You must protect them" Chuck said before closing his briefcase and leaving.

"He sure knows how to make an exit" Spencer watched as Chucks car drove away.

"He likes to think he is mysterious, he isn't" Sean laughed. He noticed Spencer making his house, as she had begun reading the files. "Well you get comfortable fast, shouldn't you be getting home?" Sean asked

"Yes, I should do that. I need to make notes about my weakness. Apparently I can be too nice for my own good" Spencer muttered standing up and putting her coat on, slipping the flies inside of her coat, then slowly zipped up her jacket. She watched as Sean had put his shoes on and grabbed a sweater. "You know you don't have to come with me" Spencer spoke giving him a puzzling look.

"Now what kind of cover boyfriend would I be if I didn't make sure you got home" Sean smiled "Besides which I don't want your Mom thinking I let you walk home on your own"

"This is true, well thank you for being such a good sport" Spencer was thankful that he had sat through a meal with her pestering mother. The two walked in silence until they reached the courtyard, Spencer felt Sean's warm hand grasp her hand. Spencer couldn't help but think back to being in high school and the awkward relationship phases of the first hand hold, she smiled and went along with it because of course it was for her cover.

"I've had a really great time getting to know you" Sean said as they reached her front door.

"Yes, it was really nice." Spencer smiled. Sean let go of her hand and went in to wrap his muscular arms around her for a hug. She really couldn't complain his hug was so warm, she felt that same comfort she had felt the first time he hugged her. As he began to release the hug, Spencer looked up at him with her big blue eyes. Their eyes made contact and Spencer wasn't sure what would happen next. They both stood silently for a few moments, Spencer wondered if he was going to kiss or not. She hadn't quite grasped the whole "cover relationship" and what it exactly entitles. When she realized he wasn't making a move she decided she would. She leaned up on her tippy toes as she was a fair amount shorter than him and gave him a simple kiss on his left cheek. As she pulled away she brought her hands to her face, wondering if she had made a mistake as he hadn't even flinched. The next thing she knew she felt his soft lips colliding with hers. He had wrapped his hands around her waist to pull her in close. She carefully placed her hands on his face.

Shortly after Sean broke of the kiss and whispered in Spencer's ear "That was perfect" before he turned and walked away.

Spencer watched as he walked away and opened her apartment door before quickly closing it. She rested her back against the door before sliding down to the ground. She placed her hands on her face and rested her elbows on her knees. "It's just a cover, just a cover" Spencer muttered quietly. She knew the only the way she could deny any feelings for Sean was to continually tell herself it was just cover she would be able to control them. She stood up, and noticed her Mom asleep on the couch. "Well I guess you're sleeping over" She muttered. Before grabbing a blanket and laying it softly over her mother and heading into her bedroom. She began to review the files she had been given.

An hour later, Sarah had awoken and noticed the light shining from under Spencer's door. Being a curious mother she wanted to find about how the walk had gone with Sean. She arose and knocked lightly on Spencer's door. When there was no answer she decided to slowly open the door in case the date hadn't ended quite yet. Much to Sarah's relief Spencer laid curled up in sitting chair of her room with a few files on her lap. Sarah was working on letting go, so she tried to deny the urge to peak at the files. _One peak wouldn't hurt_ Sarah thought as she stepped forward the floor board creaked which caused Spencer to jump.

"Mom what are you doing?" Spencer asked as she clutched the files closely.

"I thought you might be more comfortable in your bed?" Sarah asked. Spencer stood up and carefully put the files into a draw in her desk and locked the draw with a numeral lock.

"Sorry, client files they are very particular on confidently" Spencer stated before pulling the blankets back on her bed.

"I understand" Sarah stated quickly. This caused Sarah to be puzzled, Spencer had kept somethings private before but she had never seen her daughter lock her desk before. This was causing her much worry and she would get to the bottom of it.

"The spare room is made up if you want to sleep in there, much more comfortable than the couch" Spencer said before laying her head down.

 _A/N: Thank you for your feedback, I do enjoy all of your reviews. I know there are a lot of questions about why Sarah left and everything and in the next few chapters that will be discussed. Let me know your thoughts._


	4. Chapter 4: Spencer Versus the Files

**Chapter 4: Spencer Versus the Files**

The following morning Sarah awoke to the closing of the front door. She heard the door lock and she jumped out of bed and entered her daughter's room. She was very curious about these files; her determination was starting to get the best of her. The desk drawer that Spencer had locked last night was unlocked; it was just asking to be looked at. When she peaked inside, she discovered it was empty. She looked around and noticed a blank pad of paper, she ran her fingers along the top of it and noticed indents, and she carefully ripped the top piece off and left the room. Once she had stored the paper into her purse, she made one last sweep of the apartment before leaving a note on the table for Spencer.

"Hey Spen, Your apartment is great, and Sean was great as well. Thank you for a lovely evening. I will see you on Sunday" Sarah wrote before she left and headed back to Laguna Beach.

Meanwhile Spencer stood on the training floor with the other candidates Jeffery and Connor. Agent Emily Clarke was instructing them on a very unique workout plan. Unlike Jeffery and Connor; Spencer was not struggling.

"Glad to see somebody is in shape" Agent Aaron Michaels stated as he entered the room with Sean following closely behind. Spencer smirked at Sean, as she knew that she impressed the team.

"Thank you Agent Clarke for the warm up" Casey entered the room. "Today we will be practicing some hand to hand combat, to assess your level of ability."

Each candidate's handler was responsible for teaching the basics of fighting. After going through some basic moves such as punching and kicking the handlers decided to test the skills. Spencer and Sean stood across from each other and Sean started to punch. Spencer blocked the punch and followed up her move with a thrust punch to the gut and knee to the stomach. Sean pushed her knee to the side, as he did that Spencer slipped her arm under his and elbow to the cheek as she turned and hip threw him to the floor.

"Walker seems to have her combat skills under control" Casey said as he watched. "Hastings I think you might need to step up your game"

"Sorry, I've taken judo since I was five" Spencer said holding a hand out to help Sean up.

"It's all good, I did not expect the hip toss" Sean laughed.

The rest of the morning was filled with conditioning training, which was exhausting but hopefully would pay off in the future. Spencer hadn't fallen behind once as she followed the agents through a 5 mile run, and a few obstacles. The afternoon was for reviewing the files with the handlers. Spencer had a page of notes she had made about her file and the other file.

"So before we discuss your file, let's talk about the agent's file you were given."

"Well basically this girl was a badass" Spencer exclaimed. Which caused Sean to smile, Chuck joined them briefly.

"How's the file" Chuck asked

"Agent Jennifer Burton, is an amazing. Her work with this team should be framed. Basically an key member of the team. It says here, the she was your handler for a few years. How awesome was that?" Spencer spoke very fast.

"She was a treasure of the team, the reason I picked her file for you was that you have a resemblance to her and I feel that you could be a great addition" Chuck smiled. He felt bad for not sharing the entire story with Spencer, he had used one of Sarah's former alias and redacted the information about the intersect and of the death.

"I hope I can do her memory justice" Spencer responded before looking down at the piece of paper of notes she had made about her file. "Now I have a few questions for you Chuck"

"Oh boy, I knew some of the things in there would come back to me" Chuck stated

"Well there is a few facts that I don't like and I'd like to prove you differently" Spencer said confidently

"Such as?" Chuck asked

"Well first off you're missing a few points about my history"

"What am I missing?"

"It says I was raised by a single mother, which I was but as the CIA shouldn't you have some information on my father. All I know is that he was killed before I was born and his name was Stephen Walker he was a decorated war hero" Spencer stated.

"Stephen Walker is probably a very common name, so when the background was taken for you the agent that completed the search may have not been able to locate a solid history." Chuck explained

"Okay, last question. When will we be doing the DNA testing?" Spencer asked

"DNA testing?" Chuck asked

"Well apparently before you can be a true CIA agent, your DNA must be check agiasnt the databases of the NSA and CIA to ensure no threats to the country" Spencer stated

"You've already read the manual?" Sean questioned

"It was just a little light reading" Spencer responded

"Alright, we will do your DNA after a few more sessions" Chuck responded as he stood up. He began to think back to the day that everything changed. Sarah was acting strangely and kept trying to discuss something with him and never had the chance to because he had thrown himself into his work, into fixing the intersect. When he looked at Spencer all her could see was the love of his life and many of her attributes and ways of completing tasks reminded him of the strongly willed girl he had lost. He soon put these thoughts to rest as he believed that Sarah would never leave him. He must have been going crazy to believe that some girl that has had multiple checks in the database could be related to Sarah, but his thoughts would not be put to rest until the DNA testing.

Spencer thought Chuck was acting strangely, as a man the same age as her mom stared at her like a love struck puppy. She sat there quietly hoping he would walk away or something, until Sean tightly grasped her hand and pull her away from the situation.

"Sorry about that, Chuck can get a little sentimental when talking about former agents and such" Sean said.

"I figured that, it was a little awkward he like the same age as my mom" Spencer joked

"Totally understandable, why don't we get out of here. I think you've covered enough training today" Sean smiled, Spencer agreed as she packed up the files and the two left castle and headed out through the gym to the parking lot. Sean began to walk Spencer to her car again and Spencer let out a sigh of relief. "I know you're probably exhausted from today, but call me if you want to talk" Sean said giving her a hug before walking away to his car.

Once again Spencer found herself starting to feel something for Sean, and she had to reminder herself that it was "just a cover, just a cover" she muttered quietly as she got into her car. Then she muttered "Screw it" and picked up her phone and dialed Sean's number. It began to ring and she started to freak out, what if this wasn't what he meant, what if she just ruined her chances. She thought about hanging up but then she heard him speak.

"Hello?" Sean asked

"Hey, I know that this is super short notice but will you come over tonight?" She asked, begging that she wouldn't be turned down.

"That would be awesome; I'll see you in like an hour?" Sean replied

"Sounds great" She spoke before abruptly ending the phone call. As Spencer realized she only had an hour to prepare herself she rushed home to her apartment. She jumped in the shower after a long day of training; she was definitely in need for. After showering, she quickly slipped into a pair of leggings and a bright pink silk tank top. Spencer carefully curled her hair so that the rested just past her shoulders.

Sean had arrived shortly after Spencer had finished getting ready. Sean had made himself comfortable on the couch and Spencer sat on the arm of the couch with her feet on the couch. Spencer had a lot of questions about the limitations of the cover relationship, since they had missed that part yesterday and she wanted to make sure not to cross any lines, or develop any unwarranted feelings.

"So I'm just curious about our cover relationship" Spencer stated.

"I knew we should have discussed this" Sean smiled

"I'm just not sure about the boundaries associated and I don't want to…" Spencer spoked slowly as she bit her lip ever so slightly.

"It's hard not to develop feelings in these situations, out of the facility my partner and I dated for almost two years" Sean said not making eye contact with Spencer.

"We don't have to talk about this, I can only imagine the difficulty" Spencer slid down the arm of the couch to be beside Sean.

"No, I need to do this." Sean said before taking a breath, Spencer put her hand on his trying to show her support. "She decided on a mission that she would rather be a solo mission person and left me stranded in Germany with no supplies and I haven't heard from her since" Sean explained

"Sounds to me like she wasn't a the girl for you" Spencer said looking into Sean's eyes

"So that's my history with partners and cover relationships. It's hard for me to trust because of that situation. But in the right situation maybe I could be open to the possibly of a relationship beyond the cover" Sean said as he starred back into Spencer's eyes.

"I understand, so for now strictly keep it to the cover?" Spencer asked, pulling her hand away. Sean grabbed her hand and placed his other hand at the small of her back. Spencer was very confused but went along.

"I didn't say that. I'm just saying that in the right situation" Sean said as he began to lean in, Spencer nodded and shortly after she felt his lips softly kissing hers and Spencer melted into the kiss. She knew that it had only been a day since she had met Sean but she felt so connected to him.

Meanwhile back in Laguna, Sarah was debating decoding the sheet of paper she had taken from Spencer's apartment. She paced through her house carefully deciding whether or not she was crossing that line. Spencer had never been secretive about work or school in the past; something was definitely changing with her. Sarah picked up a pencil and began to gently shade over the piece of paper, to her surprize the name J. Burton was the first thing that was revealed. Sarah was in shock, had Spencer figured out her identity? Where did she find the former alias? Her curiosity fueled her need to discover the entire story. She continued shading the page, a few points about past missions. Then thoughts on strengths and weaknesses stated many thing Sarah already knew about herself. She realized in that moment that Spencer wasn't figuring out her previous life, she must have been recruited into being an agent. She reached for her phone and dialed her daughter's number. She couldn't believe it all the work she had done to protect Spencer from the life of alias and life threating life choices. The phone rang and rang, Sarah waited.

Spencer felt her phone vibrating in her pocket which caused her to release from the kiss with Sean. She looked down at the name as she pulled the phone from her pocket. It was her mom, she debating letting it go to voicemail, but before she could she decided to answer the call.

"Hello?" Spencer asked as she picked up the phone.

"We have some things to talk about" Sarah said forcefully.

"What's going on?" Spencer asked, as she stood up from the couch.

"Spencer Walker, you need to come home" Sarah said

"Mom, this unlike you, are you okay?" Spencer asked

"Everything is fine, I will see you Sunday we have a few things to discuss" Sarah stated firmly. She had decided it wasn't worth bringing this information to Spencer before she knew all the facts. Sarah may have been out of the spy game for over 20 years, but she would get to the bottom of this. She was madder at herself because she missed the signs, of her daughter being recruited. She knew she didn't have all the answers yet, but the next three days would be more than enough time to locate her handler and the operations of the headquarters.

"Okay, well I'll see you Sunday" Spencer said hanging up the phone. Spencer was once again very confused and looked toward Sean.

"Everything okay on the Mom front?" Sean asked

"I'm not sure, but I'm definitely going to get to the bottom of it" Spencer said

A/N: Thanks for all the feedback, I hope you enjoyed this chapter and let me know what you think!


	5. Chapter 5: Sarah Versus the Past

**Chapter 5: Sarah Versus the Past**

The past was a very painful thing for Sarah to look back upon. Before she married Chuck, being a spy was the only thing she could think of. Living day by day, under any alias; doing whatever it took to survive. But the day she said "I do" everything changed. She spent her nights worrying, tossing and turning about the stupidest of things, she remembered that one night so vividly. She began to think back to the day she left him, both their actions were ingrained in her mind.

After many sleepless nights she tried to tell Chuck what she was feeling. "Chuck" Sarah whispered as she rolled over in bed, only to notice that her bed was empty. She sighed this had been a regular occurrence ever since the faulty intersect was released. She carefully arose from bed and wrapped herself in a small pink house coat before exiting the bedroom. She quietly walked down the stars to where she saw Chuck asleep at his desk. She wanted to tell Chuck about the possibly of this wonderful thing that she was carrying. Sarah protectively grasped her stomach as she thought about the future.

The only thing she could not take the risk of this child growing up in this world. Chuck had been very distance lately; he had thrown himself into his work after his father passed away. Chuck wanted to fix the intersect so the future CIA would still know his father's name.

Sarah placed her hands on Chucks shoulders, she cared so much that it was hurting her to see him work this hard. She bent her knees and whispered into Chucks ear. "Hey sleepyhead I think it's time for bed" before she gently kissed his cheek. Chuck began to open his eyes, and smiled when he saw Sarah's face.

"What time is it?" Chuck asked groggily

"About 1 am" Sarah replied.

"I'll be up in a few minutes, I just have a few more things to finish up" Chuck said as he turned his attention towards his work.

"Then I'll wait here, Chuck we need to talk" Sarah said before getting comfortable in one of the empty chairs.

"Okay, I promise" Chuck muttered. After about an hour of sitting waiting for Chuck, she began doze off. Chuck glanced over at his wife and smiled, this was everything he wanted. He had felt bad about working so much but he needed to do this, so nobody else would ever experience the negative side effects or end up in a state of mind where they forgot everything. He decided not to wake Sarah when he did decide to finally head up to bed. He carefully lifted her slender body into his arms, he noticed Sarah snuggle her head into his arms. Chuck could see a small smile escape from her lips as she was comforted while in his arms. Once he laid her in the bed, he softly kissed her forehead before changing and getting into bed. As he laid back he felt Sarah squirmed into his arms, she rested her head on his chest.

The next morning Sarah awoke and realized that Chuck's side of the bed was empty. She let out a large sigh, she wasn't going to be able to hide the pregnancy much longer. She kept hoping he'd come around, and stop throwing himself into work. But clearly he wasn't ready to leave the intersect behind. She arose from bed and prepared herself for work.

Later that day she walked into castle and notice Chuck tinkering on his father's old laptop, she needed to get through to him. This life wasn't for her anymore but, Chuck was wanting to be part of this team so badly he was over working himself to prove his worth and change the way the CIA viewed the intersect and the agent that withholds the skill set to properly use it.

"Chuck, we need to talk" Sarah said as she joined him

"Sarah, Sweetheart can we talk later? I've almost figured this operating system out, which will assist in the project"

"I can't put this off anymore. I'm pregnant" Sarah muttered quietly. She looked at Chuck with the longing in her eyes to be heard, and he didn't even lift his head from his work. "I think I need to go on a mission, will you come with me?" Sarah asked, hoping a mission would be able to allow them to talk. All she wanted to do was find the right time to tell him, like how many times Chuck has tried to propose to her. She watched as he pushed his hair back with his hands, and she already knew his answer. "No its okay, It was just a suggestion. I miss being us and how we worked so well together" Sarah muttered quietly before walking away.

"Sarah, wait!" Chuck looked up and walked towards her. "Have a good mission, I'll see you when you get back" as he softly kissed her lips. Sarah was screaming on the inside, she wanted so much from him and he was so lost in his work. She wanted to tell him she wanted to leave this life, just like she told him back in the European train station. That was always stuck in her mind, he had chosen being a spy over a life with her. As she packed her bags for the mission she realized the only way to protect their child was to leave this life without Chuck. She knew that this would hurt him more, but these past few months had been so difficult with the long work hours, and with him being so busy. It also occurred to Sarah that this would affect him so much, but she had tried for so long to help him and he didn't want it. As Sarah left for her mission, tears ran down her cheeks. If Chuck ever found out what she had done, she would never be forgiven. She would spend forever missing the love of her life but she would always have a token of him, their child.

As Sarah realized she was thinking about the past caused Sarah to tear up again, she knew she had tried to do what was best at the time, but she couldn't help thinking what might have been. Now 21 years later her beautiful daughter has now entered the life that she had tried to protect her from. Sarah had grown so much as a person over the past 21 years she couldn't help think what might have been if she had stayed with Chuck.

Sarah knew that she was going to stop reflecting on the past; instead she was going to focus on protecting her daughter, to make sure it was not all for nothing.

 _A/N: I wanted to elaborate on Sarah's reasoning for leaving, as many have been curious about the why. Let me know what you think!_


	6. Chapter 6: Spencer Versus the Intersect

**Chapter 6: Spencer Versus the Intersect**

Spencer had awoken at early the next morning; her head was still reeling from the entire occurrence of the past few days. After having been recruited into the CIA, meeting Sean and the strange phone call from her mother, she found herself in a confused state of mind. As she slipped out of bed she pulled on a pair of leggings and a running long sleeve shirt, tied her Nike runners on. Running always seemed to help clear her head, that and doing dishes. As she ran is reflected on the past few days, how lucky she had been to meet Sean, and how caring and gentle he had been last night. They had hung out late into the night watching movies and cuddling on the couch. Spencer approached the beach; she sat down on the sand. The beach had been an important part of her mother's and father's relationship, in some ways she felt connected to her father at the beach. She had never met him; he died in the army shortly before she was born. There were not a lot of pictures or belongings that her mother had kept, but when Spencer had turned 10 she was given a small photo of her father. Sure it was a blurry picture that you couldn't make out his face but it meant the world to her and she took it everywhere she went. She lifted the small picture from her pocket and smiled. She had always wished she had known him. He would have been such a great father, from the stories her mother had told her.

Chuck had always found the beach to be the only place to connect with the memory of Sarah. He would sit on the beach, just like on their first date. He imagined a life where everything had worked out and Sarah was still with him. He looked over and noticed a familiar face sitting on the beach, at first he thought it was Sarah, but then as he approached he realized it was Spencer. She greeted him with a smile.

"I didn't think anyone else enjoyed the beach as much as I do" Chuck stated as he sat down beside her.

"It's a great place to think" Spencer said as she carefully folded the photo. Chuck noticed, but didn't want to pry into her life. "I just feel connected to my father, according to my mother the beach was an important part of their relationship. I did not have the chance to meet him, so this is all of I have of his" Spencer said.

"I understand, your feelings. My wife and I had loved the beach and had spent many sunrises and sunsets. I lost her many years ago so I find comfort in the beach as a piece of her is here with me" Chuck said, he had never met anyone else who had such a strong connection with a beach.

"Well I should probably get going, I need to call my mom before heading into the gym this morning" Spencer said as she stood up, she wasn't a fan of his awkward moment she was sharing with her boss.

The next few weeks of training were probably the best few weeks of Spencer's life, she had really pulled ahead of the other candidates and had a really good feeling going into the final day of training. Spencer had been so busy the past few weeks she hadn't been able to visit her mother, but had promised herself once she made the team she would. As Spencer prepared herself for this final day, she heard a knock at her door. It was her mother.

"Hey Spencer, long time no see" Sarah said pushing past Spencer and into the apartment.

"Sorry, you know I told you work has been crazy busy" Spencer apologized.

"Well I thought we could do something today?" Sarah asked with a smile

"I should be able to after work today" Spencer stated. "Just hang out here and I'll be back in a few hours" Spencer said before grabbing her bag and headed off to work. Sarah was going to confront Spencer when she arrived home. Spencer's tendency to overreact was definitely a Bartowski trait she had inherited.

Spencer arrived at castle and noticed that it was the other agents, Chuck and Casey. She looked around for the other two candidates. "They aren't here" Sean smiled.

"Congratulations Miss Walker you have been chosen to be the next agent and asset to this team" Casey smiled.

"This is wonderful, I can't believe it" Spencer said.

"This team is not like any other CIA team. You have been specially accepted into a specialized team. If you agree to it you will be the next intersect" Chuck grinned.

"Intersect?" Spencer asked

"Basically a bunch of encoded government secrets are put into your brain" Sean said as he put his arm on Spencer.

"And this will make me an asset to the team?" Spencer asked

"You will one of the best asset's we've ever recruited." Chuck smiled

"That's why we put you through training to make sure you had what it takes, but you have much more to learn" Casey said.

"Well, if I've been chosen then I will accept this honour." Spencer smiled as she realized she was about to serve the greatest honour for her country. Chuck showed Spencer to a room and sat her in a chair.

"Now I know that this seems a little fast, but we have been without a intersect for many years. You will be briefed on your agent duties and all other testing, like the DNA testing will be complete in the next few days. This will give you a chance to get a handle on the intersect" Chuck said as he disappeared into another room.

"So what is going to happen?" Spencer asked

"There is going to be a lot of images shown to you, it takes about an hour or two depending" Chuck said.

"Okay will let do this" Spencer said as she sat comfortability in the chair as she waited for it to begin.

"Alright, and we will be starting now" Chuck said as he had pushed the button. The CIA had not been able to find many brains that could withstand the intersect, many of them were actually put into mental hospitals as it was too much for them. He hadn't trained or chosen those applicants, he was very hopeful for Spencer. He had a feeling she was going to great things as the intersect. He watched as Spencer sat in the chair and was taking in at the images.

As the upload finished Chuck, Casey and Sean, stood around waiting to see the results. Spencer stood up and fell backwards with a loud thud.

"Well, she had the same reaction as you" Casey laughed

"That is a little strange, but maybe a good sign" Chuck smiled as he knelt down beside Spencer. Sean was pacing at her feet as he waited to see if she was going to come to.

"Hey Hastings, do you mind. You're kind of distracting" Casey stated as he starred at him.

"Sorry I'm just nervous" Sean spoked as he stopped pacing. Spencer begun to open her eyes, brought her hands to her head as she sat up.

"I feel like I was hit by a truck" Spencer muttered.

"You're okay!" Sean smiled and looking longingly towards Spencer.

"Of course I'm fine" Spencer stood up.

"You should be a little careful, It might take some time for your body to adjust" Chuck watched Spencer carefully.

"I'm fine, I have some plans with my Mom. Am I able to go do that?" Spencer asked

"Yeah you should be able to do that, but take Sean with you just in case you need any help" Chuck said as he kept an eye on Spencer.

Spencer nodded, she felt different, and she felt useful. It was going to be a very interesting next few days; she had this think in her head and had no idea what was going to happen next.

"Sean I'm fine you don't need to watch me like I'm going to break" Spencer said as she stepped out of his car.

"I have my orders" Sean said as he quickly got out of the car and followed closely behind her.

"So now I'm your orders?" Spencer questioned. The past few weeks had been so great with Sean. Although they had been seeing each other outside the cover, but hadn't really defined if it was anything or if they were going to continue not to discuss and pretend like everything was fine.

"That's not what I mean, we just have to be careful especially now" Sean said as he grabbed her hand. Spencer pulled away.

"Or we could not be careful" Spencer said as she continued to walk to her apartment. Sean followed in silence he did not want to get into this at this moment. As they reached the door, Spencer turned around and faced Sean.

"I'm sorry, Babe. You know that I've been enjoying this and I just want to make sure you're okay" Sean looked apologetically towards Spencer.

"I'm just processing, a lot has happened today. Just let's get through this evening and we can talk about this later" Spencer said as she reached for the door knob. Sean slipped his arms around her waist and leaned in to kiss her. Spencer accepted, she wrapped her arms around his neck and became lost in the moment. She broke the kiss apart and muttered to herself "Well that is definitely the reason we haven't talked." She couldn't argue with the way Sean decided to cover their disagreements. Spencer turned the door knob and walked into her apartment, the sweet smell of pork roast. "Mom, I'm home and I brought Sean" Spencer said as she looked around and noticed the table was set.

"That's great Spen, I'm just taking the roast out." Sarah called from the kitchen. Spencer entered the kitchen and paused, she saw many images of her mother continued through her head. There were a few that stuck out to her. She saw her mother sitting at a table with a bunch of diplomats that all collapsed after eating the soup, a few different names popped up; Jenny Burton, and Sarah Walker. The last image she saw included information that stated CIA agent, and missing in action, presumable death. Spencer took a step back and her entire demeanour changed, she quickly left the kitchen.

Sarah had seen the look on Spencer's face, it reminded her so much of Chuck. Sarah took a moment a realized what that look meant, at least to Chuck that had meant he had just seen a flash. Sarah took a deep breath and realized, no there was no way. She had waited too long to confront her, if it was any normal CIA training she would have had a few more months. This must be the intersect and now Spencer had seen everything she had ever done. Before she had a chance to explain, this may have just ruined everything

Spencer pulled Sean into her room and shut the door. "We have a problem"

"Are you okay?" Sean asked

"My Mom, is that agent J. Burton" Spencer said quietly.

"Holy, that is so cool she is such a badass!" Sean smiled

"No not cool, she is apparently dead. But she isn't, she is right here" Spencer explained.

"You had a flash?" Sean asked.

"I guess so, but what are we going to do?" Spencer asked

"I'll call Chuck. He'll know what to do." Sean stated reaching for the phone. Until they heard a knock on her door and it slowly began to open. Spencer acted quickly and kissed Sean passionately.

"Dinner is almost ready; I hope you guys are hungry" Sarah said as she peered into the room. "Oh I'm sorry" Sarah said as she quickly turned around. She knew she need to talk to her daughter about everything, but she couldn't help but bit a little proud noticing the cover technique she had just utilized.

 _A/N: Thanks for everyone's feedback, I know that many of you aren't impressed with Sarah's actions but there is still more background information coming in the next few chapters. I hope you enjoyed this chapter and can provide more feedback._


	7. Chapter 7: Spencer Versus the Truth

**Chapter 7: Spencer Versus the Truth**

Spencer paced in her bedroom, before finally getting a handle on the feelings that had occurred in the past few minutes. After realizing that the awesome agent that she had been researching was actually her mother, was mind blowing. Her mom went to yogalaties and worn her pyjamas until noon on the weekend, there was no way that could have been her Mother, the intersect must be faulty.

"Call Chuck, I'll distract her" Spencer turned to Sean before exiting the room. Spencer walked into her living room and saw her mother. "Dinner smells amazing and sorry about that Sean and I hadn't seen each other in a few days" Spencer lied through her teeth. She was very curious about this entire ordeal but first thing first was keeping her mother unknowing.

"Don't worry about it sweetie, I remember young love" Sarah smiled as she began to pace in the living room.

"Mom is everything okay?" Spencer asked.

"I need to tell you something" Sarah spoke slowly. "Before you were born I made a decision, for which I thought it was for the best"

"Okay"

"I left a part of my life behind and I've regretted it. I left to keep you safe, the situation at the time felt unescapable"

"Alright"

"I was an agent for the CIA" Sarah stated. Spencer nodded. "But you already knew that"

"Why do you think that?" Spencer questioned as she didn't want to blow her intersect identity already only a few hours in.

"Your father used to get the same look when he got a flash" Sarah whispered

"Wait my father was an intersect?" Spencer asked

"He was the first" Sarah said slowly

"Has everything you've ever told me been a lie?" Spencer questioned

"I thought I was protecting you from the life I had. I hadn't had a home until I met your father, and I began to put down roots and I got scared, things went so fast that year" Sarah said.

Just then there was a knock at the apartment door. "I'll get that" Spencer said walking towards the door.

"Who is it?" Sarah asked

"It's my boss" Spencer said as she opened the door. "Hey, come on it" Spencer said as Chuck walked past the door. He made eye contact with Sarah and he almost began to melt, she hadn't changed much other than her hair colour, of course. After all these years she was here, he walked over and hugged her.

"You're alive" Chuck whispered in her ear. "Wait, how and why?" He stepped back as he realized the situation he was in.

"Spencer I have lots to explain, but first let me talk to Chuck" Sarah said as just tugged Chuck's arm so that he would follow and closed the door to the spare bedroom. As soon as the door closed, Spencer and Sean put their ears to the door.

Spencer was very confused how did her mother know Chuck, and why was he so shocked to see her. As she thought about it, it triggered another flash. This time it was about Chuck and her mom. They had been partners, wait no she was his handler and he was the intersect 1.0. She gasped as she made the realization that Chuck was her father. This only brought up more questions and she was going to find out the answers.

"Sarah, I've missed you so much" Chuck said with his puppy dog look.

"You are going to regret that" Sarah said

"What do you mean?"

"Chuck, I left you that solo mission I went on, I used that to leave" Sarah said firmly.

"But why Sarah?" Chuck asked longingly

"I wanted to protect our daughter" Sarah said

"Our daughter?" Chuck asked

"Spencer is yours" Sarah said as she sat down on the bed.

"You took her away from me, but I don't understand. Before that mission everything was so great." Chuck said with a look like he had been spent years looking for a woman who didn't want to be found.

"I didn't want that life for her, and I had tried to tell you. But you were so wrapped up in the new intersect that I didn't know how to break it to you" Sarah said

"This is all strange, Sarah you were all I needed in life, I would have gone with you" Chuck said

"Chuck, after your father died, you changed. I spent weeks trying to figure out the best way to tell you and I couldn't. I had visions of the train station where you didn't want to run away"

"I understand, but I hope you know that I regret spending the last 20 years looking for you, for answers and this wasn't the answer I hoped for." Chuck said as he turned to leave

"Chuck wait, I take responsibility for this. I know you won't be able to forgive me, but I'm hoping that you will still accept Spencer as she probably won't speak to me every again." Sarah explained

"Sarah I may never forgive you, but if the last 20 years have taught me anything. Mistakes happen and I've spent to long without you in my life, to have you completely out again. I'd rather have you around to hate, than not to have you around at all. You'll be coming into castle and having a chat with Beckman, as you are considered a rogue agent. As for Spencer, you did well with her, she reminds me so much of you" Chuck said before leaving the bedroom. As he opened the door, Sean and Spencer jumped back and pretended to be in conversation. "Spencer I guess you probably heard. I know that this is probably overwhelming, but when you want to talk. I'll be there. Agent Hastings, once they have had talked, I'd like you to bring Sarah Walker into castle." Chuck said before he left the apartment. Chuck was furious, he had spent all this time trying to figure every single detail out about Sarah and the final message only to realize that it was all an elaborate ruse for Sarah to once again run. But what he had said to Sarah was true, he had missed her so much, and just wanted to be around her even if it meant he hated her. He reflected on the last few weeks Spencer, she really was a great young woman, Sarah had done a great job raising her.

Sarah appeared from outside of the spare bedroom, and watched as her daughters eyes filled with tears. Sarah stepped forward to try and comfort her daughter. Spencer stepped back closer to Sean, who put a protective arm around her.

"Chuck was an intersect and you was his handler, you told me my Dad was dead" Spencer said as she pulled out the tiny blurry picture she had. "You said this was him, you said that he was dead. He has been here the entire time, and you lied. All those times I asked about him, were they all lies?" Spencer continued. "Is there any truth to anything in my life?"

"Spencer Elizabeth Walker, there is so much you don't know" Sarah said.

"Then enlighten me?" Spencer stated firmly.

"It was a long time ago, but I didn't want this life for you. I wanted you to be normal, grow up and be safe. Being a agent with the CIA is very serious, and with a mind like yours you would have been on there radar before you turned ten." Sarah started. "Your father never knew the reason why I left, he thought I was dead. He had finally become something greater than working at the Buymore and I didn't want to change his life." Sarah sighed. "It was probably the worst decision I've ever made, but once I had left things just seemed easier"

Spencer tried to hold back her tears; she buried her heads into Sean's chest as she tried to collect herself. "I just wished you hadn't kept this from me"

"I know that this is a lot and just know that I love you and will always love you. You have grown up and become such a lovely young woman and I couldn't be prouder. I know that you may never forgive me but I hope someday you can see the situation through a different lens" Sarah said, her eyes began to water. She never realized how much this would hurt Spencer, she thought she was doing the best she could, and she still messed up.

"Let's go to castle" Spencer said as she dried her tears on a tissue.

"Sweetheart, you're not supposed to over stimulate today, you know because of the…" Sean muttered in Spencer's ear.

"You really don't think I'm going to miss any of this right?" Spencer said as she grabbed her coat. Sarah stood awkwardly waiting. As they headed out to the courtyard, Sean still followed Spencer closely. "Would you stop watching me like I'm going to break, I can walk I'm fine" Spencer said, Sean took the queue and walked ahead of Spencer and Sarah.

"So how long have you had feelings for you partner there?" Sarah asked

"I don't want to talk to you about this, you lied to me for 21 years" Spencer said

"Just be careful partnerships that turn into relationship can be difficult, especially when there are feelings involved" Sarah quietly said.

"I didn't ask you, this is my life and you have already messed it up enough" Spencer said as she reached Sean's vehicle. Sarah got into the backseat and sat quietly, she could hear Sean and Spencer argue about a few things, they sounded just like how she would argue with Chuck.

"I'm worried about you" Sean said as he walked over to the side of the car Spencer was standing at.

"I'm fine, really. I need you to just let me figure this out" Spencer said.

"You know I care about you, and right now this isn't you" Sean said as he stepped closer, as he went to pull her closer to him.

"I just feel that my world is crumbling" Spencer looked up at Sean

"Let me be your rock, I'll stay with you until you feel that your world is safe" Sean whispered in Spencer's ear. Which caused her to slightly smile; he leaned down and gave her a soft kiss.

"Thank you, I needed that" Spencer said as she wiggled her way out of his arms and into the car. They drove off towards castle in silence.

A/N: I am very grateful for everyone's feedback, I know that I could have taken this story in many different directions. But I this just seems like the way to go for now.

Now about this chapter I know that it seems like Chuck has forgiven Sarah, but trust me he hasn't. In the next chapter I will definitely touch on that, plus Casey and Beckman's reactions with definitely push Chuck over the edge. Let me know what you think, I'm open to everyone's feedback!


	8. Chapter 8: Sarah Versus the CIA

**Chapter 8: Sarah Versus the CIA**

Sean and Spencer escorted Sarah down into castle. Before entering castle, Sarah grabbed Spencer's hand, Spencer turned and made eye contact.

"Baby Girl, you need to know I'm so proud of everything you have done. I'm even prouder that on your own you were recruited to the CIA. I just wanted to tell you that" Sarah spoke slowly.

"All I have ever wanted to hear was that you were proud of me. I've spent my life in a lie, and I can't help not trusting you." Spencer said pulling away and opening the door. They sat Sarah down in front of the large screen. Casey walked in moments later.

"Walker, out of all the agents to go rogue, I never thought it would have been you" Casey said as he made eye contact with her. Sarah nodded, but stayed silent. Chuck sat at the computer at the side of the room, he hadn't moved since Sarah had entered. The telephone beside him rang and he picked it up.

"Yes, this is Bartowski. She is present…. Hastings, Casey and Spencer Walker are present… Alright" He hung up the phone and turned the chair. He made sure he didn't make eye contact with Sarah. He could feel the rage inside him growing. He didn't understand her reasoning, but knew that he needed to stay strong especially in front of Beckman and of course his daughter.

A picture of the red headed director appeared on the screen. "Sarah Walker" Beckman said.

"Hello, Director" Sarah looked up.

"I've been briefed on the information given by Agent Bartowski and I can't help but be a little surprized by your actions" Beckman continued.

"Yes, Ma'am" Sarah responded.

"Spencer Walker our newest addition, is your daughter?" Beckman stated

"Yes, Ma'am"

"Agent Hastings, has Spencer shown any difficulties this afternoon?" Beckman asked

"She has been adjusting to the transition, and was able to flash on information about her mother, which lead us to the discovery" Sean responded.

"Director, this has not affected my ability to be an Agent on this team. I'm just as surprized as everyone to find out my Mother was a rogue agent." Spencer interrupted. She crossed her arms as she looked over at her mother.

"Spencer, no one is questioning your ability." Chuck responded.

"Spencer Walker, we are very happy with the results from your training. If we could please stay on topic" Beckman stated. "I would like a detailed report of your interrogation Agent Casey of Ms. Sarah Walker."

"Come with me, Walker" Casey said as Sarah followed him into the interrogation room.

"Agent Hastings, please escort Agent Spencer Walker to her apartment. Walker, your rest and abilities to highly important to this program, I know that a lot has occurred in the past few hours and has raised many questions" Beckman stated

"Director, may I ask a question?" Spencer asked

"Yes"

"I'd like to stay, I feel that I will be able to collaborate and be able to assist this interrogation. I have already had two flashes on things from the past about my mother" Spencer clearly described the two flashes she had, Beckman nodded and allowed her to stay. Spencer shortly exited the room, Sean following closely behind.

"I feel that Walker is a good match for Hastings. I haven't seen him this involved in his work since he joined this team" Beckman stated. "Bartowski, you must be extremely conflicted about this whole situation. You give the word and we will transfer Sarah to another team"

"No, Sarah stays here. I have so many questions" Chuck clearly stated.

"Alright, Bartowski. Sarah is in your team's custody until her hearing with the board." Beckman signed off and the screen went black.

Chuck sat in shock, Sarah was alive and she had kept so much from him. He knew he needed to talk to Ellie about this; she would help him decide what to do and how to act around the woman he loved so dearly. She lied for over twenty years, and he didn't understand her reasoning whatsoever. He would get to the bottom of this. He stood up and walked over to the interrogation room, and stood on the other side of the two way glass, beside Spencer while Casey began his interrogation.

Sarah sat patiently, as Casey hooked her up to a lie detector.

"Casey this isn't really necessary" Sarah was very confused, in her day she would have just scared the accused.

"It's new policy for all rogue agents" Casey muttered quietly. "Walker, please tell me the events of your last mission"

"The mission, alright, I was to get close to a French nationalist to figure out their relationship with the Paris mob. They had been getting quite aggressive lately, so I had to make sure I was on the top of my game. I had been doing quite well getting close and working the angles when I was walking back to the hotel after attending a dinner, I was attacked. I was mugged, but this mugger wasn't any run of the mill mugger. He was trained very well and somehow got the upper hand on me. I fell to the ground and laid lifeless, as I hoped for no more beating to project the fetus inside me."

"What happened next" Casey asked

"He had taken my wallet and my phone, it was the perfect chance for me to fall through the cracks and leave the CIA"

"You knew you were pregnant prior to taking the mission?"

"Yes"

"Have you ever done something to break the code of conduct?"

"Other than being a rogue agent, I haven't given up any secrets"

Spencer and Chuck stood on the other side of the mirror. Chuck's face started changed, the angry was starting to show. He had processed the information and now he was furious. He turned and walked through the door.

"How could you?" Chuck said as he slammed the door behind him

"Bartowski" Casey stated

"Save it Casey, I deserve some answers"

"I don't understand, we were so good" Chuck stated

"I know, looking back I probably could have done things a lot differently" Sarah's eyes began to water.

"DO YOU KNOW HOW LONG I LOOKED FOR YOU?" Chuck raised his voice, making it apparent that he wasn't accepting her excuses.

"I didn't think that you would look for me" Sarah muttered

"I loved you and you vanished, of course I would look for you." Chuck sat down in front of Sarah.

"I still love you" Sarah muttered

"Doesn't matter, what you have done has been unforgiveable" Chuck starred at Sarah

"I'm so sorry, Chuck"

"It's a little late for apologies, you'll be spending the next twenty years thinking what could have been" Chuck stood up and left the room. Sarah sat there with tears streaming down her face. In that moment she realized something she had not thought of for a long time. She was so worried about their child that she took everything that could have meant something to him away, she had been so selfish and ruined everything that might have been.

 _A/N: Sorry it's been a few days I was away for the weekend, but I finally wrote another chapter! Hope you enjoy, thanks for all the feed back!_


	9. Chapter 9: Spencer Versus the Family

**Chapter 9: Spencer versus Family**

* * *

A few weeks had passed since CIA had taken Sarah Walker into custody, after a week or so of reviewing and testing her skills and knowledge. Sarah had been cleared to train and asked to work as an analyst within the intersect team. Although Spencer and Sarah hadn't had much contact the CIA felt having Sarah present would increase the team's productivity, as Sarah knew the most about her daughter.

Sarah had been staying in castle temporarily until her housing situation could be figure out, the CIA had wanted to place her with Spencer, but Spencer had declined all attempts as she needed some well needed space from her mother.

Chuck hadn't said much to Sarah, he had kept his distance as he was having difficulty understanding his feelings. After his outburst during Casey's interview of Sarah, he had realized he needed to figure out his own before approaching the subject again. On the other hand, Spencer and him had gotten close. Not weirdly close, just close enough to discuss some factors of her personality and traits she had gotten from him.

* * *

Spencer had just entered Castle and was greeted by a smiling Chuck.

"Good Morning!" Chuck smiled.

"Hi" Spencer waved.

"So, Spencer I was thinking we've been discussing family lately…" Chuck began to say

"Yes Ellie and everyone?" Spencer said

"Well, I was thinking if you wanted to meet them?" Chuck asked.

"That would be really cool" Spencer stated.

"Okay, we usually do a family dinner on Friday's" Chuck smiled.

"So tonight?" Spencer asked.

"Is that too soon?" Chuck asked.

"No that would be nice" Spencer said. She really did appreciate Chuck for trying to make a relationship with her.

"Perfect" Chuck smiled. He had mentioned to Ellie briefly that he may have found his daughter, but hadn't mentioned that he had been spending time with her or that she worked with him. Ellie didn't like his own involvement in the CIA.

Sarah exited her sleeping quarters and walked slowly over to the gym, she passed Chuck and Spencer discussing plans. As she approached them, both got quiet and went separate directions. Sarah caught up to Spencer.

"Hey Girly, how's it going?" Sarah asked hoping Spencer would respond.

"Hi Mom, it's going." Spencer abruptly responded.

"That's good" Sarah half smiled.

"Sorry, I've got to get a 5 mile run in before I meet up with the team" Spencer stated before heading towards the treadmill.

"Oh okay, maybe can we do dinner tonight?" Sarah hoped.

"Sorry, I've got plans." Spencer put her headphones into her ears and began her run. Although she was still processing her mother's actions and reasons; she did miss having there chats. Spencer began to worry that Chuck's family wouldn't like her, besides which for over twenty years she only had one person she could count on, her mom. She missed her mom greatly; they had a great bond before all this came to light. She had realized that pushing her away would only lose another relationship instead of moving past and growing from her mother's mistakes.

"I understand" Sarah muttered, as she sat down at a rowing machine.

Spencer stopped mid run and went over to Sarah, she realized shutting her out wasn't the answer.

"I may not forgive you, but I need your opinion and assistance" Spencer said heavily.

"Okay" Sarah looked up as she wiped the sweat from her face.

"Come by after work?" Spencer asked.

"I will be there" Sarah smiled.

"Alright" Spencer said walking back towards the treadmill. Sarah smile grew as Spencer walked away, she had finally reached out and she wasn't going to make any more mistakes.

* * *

Chuck stared at his computer screen for what felt like forever, before her picked up the phone and dialed Ellie's number.

"Hello?" her light voice answered.

"Hey Ellie" Chuck replied

"Chuck, hi. You better not be cancelling tonight's dinner!"

"No that's not why I'm calling"

"Oh good"

"So Ell-, how would you feel about me bringing someone with me tonight?" Chuck asked

"Well…. Finally" Ellie exclaimed. "Is this the mystery girl you've been spending all your time with?"

"It is" Chuck replied

"This is great, I'm so happy you've found someone, I've been so worried about you"

"I'm not bringing a girlfriend" Chuck explained.

"Then who?"

"My daughter" Chuck muttered

"You've been spending time with her, and this is the first I'm hearing of this" Ellie yelled, Chuck pulled the phone away from his ear.

"Sorry, I didn't want to mention anything."

"I'm still in shock, that Sarah lied" Ellie replied.

"As am I" Chuck retorted. He hoped Ellie wouldn't poke around with many questions as he hadn't explained the whole situation to his sister, as it is kind of classified.

"Okay, well I've got a patient to see, but I'll see you tonight" Ellie hung up the phone.

* * *

Later that day, Spencer stood in her apartment she had laid a few different outfits out on her bed and was waiting for her Mom. She soon heard a light tap on the door, she ran to get it.

"Hi Spen" Sarah smiled.

"Okay so I needed a mom chat before tonight" Spencer said in a panic.

"What's up?" Sarah asked.

"Well, I'm meeting-"Spencer began to say.

"Sean's parents, it's a cover Spen. You don't actually have to meet the parents" Sarah smiled.

"No, I'm meeting Chuck's family" Spencer muttered.

"Pardon?" Sarah replied

"I'm meeting Chuck's family" Spencer repeated louder.

"Oh that's so nice, I'm happy for you. Ellie and Devon are lovely" Sarah smiled.

"I was hoping you could help me pick out an outfit?" Spencer asked.

"Of course sweetheart" Sarah responded. Spencer led Sarah into her room and showed the outfits she had laid out. After much bricking they decided on a pair of black jeans, with knee high boots and a nice blouse. Sarah helped Spencer curl her hair, as Spencer did her makeup.

"This was nice" Spencer muttered.

"I missed this" Sarah replied.

"Mom, I know I won't ever understand your reasoning. But I know I will need you" Spencer answered.

"Kiddo, I'll always be here"

"I was thinking, staying in castle must suck. So you can stay here temporarily?" Spencer asked.

"But before you-" Sarah began to say.

"Let's not worry about before, I'm still processing but a girl needs her mom sometimes" Spencer interjected.

"Alright Girly" Sarah smiled. Spencer had finally come around, they definitely still had their challenges but at least this was a start.

"Mom, what if they don't like me?" Spencer asked.

"Spencer Elizabeth Walker, you're so much more than worrying about if they will like you. Which they will, because who couldn't love that face, just be yourself and everything will work out" Sarah replied.

* * *

Spencer sat in her car, debating if she was to go into her aunt's home, or wait for Chuck. She gently tapped the steering wheel debating, when her phone chimed. It was from her mom, " _stop wait and just go in already"_ Spencer looked over her shoulder and didn't see anyone. She quickly dialed the phone.

"Mom are you stalking me?" Spencer asked.

"No, I just know you" Sarah replied.

"Oh, alright. I'm not sure if I was to meet him or go in?" Spencer asked.

"Such a dilemma"

"But really?! It will be really awkward if I go in with him" Spencer exclaimed.

"Take a breath, it won't be hard to get through this" Sarah replied

"That's safe for you to say, you're safe in the apartment away from this situation" _Knock. Knock._ Spencer turned her head to notice Chuck tapping on the window of her car. "Uhm, well I've got my answer talk to you later Mom" Spencer said hanging up the phone and getting out of the car.

"Were you debating whether or not to go in as well?" Chuck asked.

"Kind of. Wait why would you be debating?" Spencer asked, as they made their way to the front door.

"I wanted to make sure you actually made it inside, I mean although half your genetics are Bartowski. The other half may have caused you to worry about how the whole situation would go" Chuck explained as he knocked on the large wooden door.

"That is a huge possibility." Spencer smiled. They were soon greeted by the smiling face of Ellie and Devon.

"Oh my gosh, you are so much like S…" Ellie began to say and then stopped.

"I didn't get my good lucks from Chuck" Spencer replied.

"Oh thank god, because all day I was picturing the female version of him and I was worried" Ellie laughed.

"My name is Spencer, and thank you for letting me into your home. Mr and Mrs. Woodcomb" Spencer said as she stepped into the house.

"Please call me Ellie" Ellie replied as she took Spencer's coat. Devon showed Spencer into the living room with Chuck and Ellie following closely behind. Spencer looked around at all the phone frames that lined the room.

"That's our daughter Clara, she is off in medical school in New York" Devon pointed.

"That's so awesome" Spencer replied.

"You really must be Chuck's kid" Devon smiled. Spencer suddenly was really confused.

"I call Devon Captain Awesome" Chuck interjected as he noticed Spencer's confusion, she nodded.

They sat down, and Ellie offered to get everyone some refreshments. Chuck and Devon both asked for a beer, and Ellie poured some white wine for herself and Spencer. Spencer clutched tightly to the glass, this might be her saviour of the night if things do go well.

"So Spencer will you tell us about yourself?" Devon asked

"I'm an open book ask me any question" Spencer replied. She knew there was obvious things she couldn't answer, like the whole thing about being the intersect but she would fill them in as much as possible.

"Where do you work?" Ellie asked.

"I'm a personal trainer at the gym over in the Buymore plaza" Spencer lied, but she knew she needed to keep her cover intact, Chuck nodded.

"Where did you grow up?" Devon asked.

"Well we moved a lot so pretty much everywhere, the last few years were in laguna before relocated to Burbank"

"Do you have a boyfriend?" Ellie asked.

"I do, His name is Sean. We've only been dating for a little while but he is a great guy" Spencer replied, Chuck noticed the spark in her eye when she mentioned Sean.

"That's great, we will have to meet him sometime" Devon replied.

"Do you have a good relationship with your mother?" Ellie asked. Chuck watched as Spencer's face changed.

"Yes and no, I don't understand her past decisions, and why she did what she did. But, she has always been there for me and was my only family for so long, I can't just forget about that." Spencer replied.

"Did you know about Chuck being your father?" Ellie replied quickly. Spencer's face went bright red.

"Ellie, let's just enjoy the evening and not pester Spencer about Sarah. What has been done is done and it wasn't her fault." Chuck interrupted. He had noticed Spencer becoming uncomfortable. Chuck knew that Spencer had believed her father had died many years prior, so he found his sister questioning over bearing and wanted to protect her.

"Sorry, Ellie can get a little heated when it involves the past" Devon apologized to Spencer.

"It's all good, everyone is entitled to their questions." Spencer answered.

Dinner was ready shortly after Ellie and Devon had concluded their questions for Spencer. At this point Spencer was able to relax a little more and enjoy herself, with the family she'd never thought she'd met. As the evening came to an end, Spencer thanked Ellie and Devon for the hospitality and agreed to attend the next dinner. Somehow they had convinced her to bring Sean as well. Spencer couldn't help but smile as she felt welcomed, it was nice to know that even though they had just met her they had been very inviting for the most part. Ellie had begged Spencer to have lunch with her in the coming days, a girls day as you would say. She had played if off that she missed her own daughter and needed someone to do girly things with, Spencer had accepted with a smile.

* * *

Somewhere along the drive home, Spencer had realized that she not only had a father now but an aunt and a uncle, and a cousin that she would eventually meet. When Spencer arrived back at her apartment later that evening, she walked in with the biggest smile she had ever had. Sarah sat on the couch reading and greeted her as she entered.

"How was it?" Sarah asked.

"It was a lot, but I really enjoyed it"

"I'm glad" Sarah smiled.

"Alright, well I'm going to go to bed." Spencer headed off to her room for the night.

Spencer ran her hand through her hair before laying down into bed, today had been an important day for her. But the next week was going to be even more important as she was preparing for her first mission as the intersect and as an agent.

* * *

 _A/N: Hey guys! So I hadn't written a chapter in a while so I wrote an extra-long one for you all! So I have a mission for my readers, I'd like some input on potential first mission's for spencer! So let me know your input and also what you thought of the chapter! Thanks!_


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